Implementation of the Avera/Sema4 oncology and analytics protocol (ASAP).
Authors: Casey B. Williams, David Starks, Rachel Elsey, Tobias Meissner, Benjamin Maurice Solomon, Melanie Albano, Feras Hantash, Eric Schadt, Luis Alexander Rojas-Espaillat, John H. Lee, William K. Oh
Journal: Journal of Clinical Oncology (2022)

TPS6605 Background: Precision medicine represents a new era in oncology and population health. Comprehensive molecular profiling and hereditary cancer testing are increasingly important in the routine management of many malignancies, yet may not be widely adopted in many practices and leads to patients not consistently receiving care recommended by current national guidelines such as NCCN and ASCO. In addition, available targeted DNA sequencing panels may be limited to only defined drivers and lack detection in precancerous conditions. Whole exome sequencing (WES) combined with whole transcriptome sequencing (WTS) represent an expanded testing approach that identifies additional genetic changes beyond standard commercial panel tests. Current evidence suggests that WES/WTS is feasible to carry out in routine clinical practice, with improved detection of somatic alterations compared to smaller panels, and the promise to enhance access to targeted therapies and clinical trials. The primary purpose of the ASAP study is to understand the breadth of molecular characteristics present in participants cared for in a large integrated community-based health system, by linking comprehensive molecular profiles with clinical data extracted and curated from the electronic medical record. Methods: Avera Health is a large, Midwestern, predominantly rural vertically integrated health system with six regional cancer centers and over 40 oncology outreach sites across South Dakota and surrounding states. The ASAP study was initiated in November 2021 in GYN and as of February, the study is enrolling in the Otolaryngology clinic and expected to open in medical oncology and hematology in March/April 2022. The study will expand to include additional cancer centers outside of Sioux Falls later in 2022 and is anticipated to be open for accrual for 5 years. Enrolled participants are expected to receive WES/WTS and proteomics on their primary tumor and metastatic sites were feasible as well as hereditary testing, pharmacogenomics (PGx) and microbiome profiling. Liquid biopsies will be performed every 3 months while on treatment or when treatment is changed, in follow up to coincide with scheduled radiographic testing, and as part of annual routine surveillance. For participants not diagnosed with cancer, each participant will receive hereditary testing, PGx, microbiome, and a liquid biopsy at least annually. Participants also consent to sharing their electronic health information. Future stages of this work will employ natural language processing (NLP) methods to develop algorithms to help identify opportunities to improve patient outcomes. Projected enrollment is 1000 participants in year 1, 1500 participants in year 2, and up to 3000 annually thereafter. Approximately 50 patients have consented as of February 1 2022. Clinical trial information: NCT05142033.